AdultAnnualSurv: Conversion of adult capture data into the correct format for...

In khuggler/Ovis: Tools to Manipulate, Collate, and Analyze BHS Data from Idaho and Wyoming

Conversion of adult capture data into the correct format for modeling annual survival

Description

Convert capture and cause-specific mortality data of adults into the proper format for conducting survival analysis.This function will convert raw data that contains start dates and mortality dates of individual animals and transform it into the proper format required by package survival to model annual survival.

Usage

AdultAnnualSurv(dbpath, mortcol, dateformat, yearstart, yearend, idcol,
  capcol, fatecol, censors, plot, title)

Arguments

dbpath	path to data.frame (csv) that contains a column of unique animal identifier, start date, mortality date, and cause of mortality (if applicable). If mortality has not occured, mortality date will be Sys.Date(), and event indicator will be 0
mortcol	name of column where mortality date exists
dateformat	format of mortality and capture dates
yearstart	year (YYYY) to begin modelling survival.
yearend	year (YYYY) to end modelling survival
idcol	name of column where unique animal identifiers are located
capcol	name of column where capture date is stored
fatecol	name of column where fate/cause of mortality occurs
censors	vector of causes that require censoring (e.g. collarfailure, capturemort, etc.)
plot	logical. TRUE/FALSE. If TRUE, function will generate bar plot of yearly survival
title	desired title of survival plot (character)

Value

Returns a data.frame with animal ID, start date of modeling, end date of modeling, status of animal (alive = 0, dead = 1), and number of months alive during time period

Examples

AdultSurv<-AdultAnnualSurv(dbpath = 'C:/Desktop/yourdb', mortcol = 'MortDate', dateformat = "%m/%d/%Y", yearstart = 2019, yearend = 2020 , idcol = 'AID', capcol = 'CaptureDate',fatecol = 'Cause', censors = c("CollarFailure", "CaptureMort"), plot = TRUE, title = 'Survival of Bighorn Sheep')

khuggler/Ovis documentation built on Nov. 30, 2023, 7:41 p.m.